Experiment: 3DB9

Crystal structure of UPF0317 protein Atu3911 from Agrobacterium tumefaciens. NorthEast Strcutural Genomics target AtR186

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PIF	2PIF.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	200 mM NH4SO4, 20% PEG 4000, 50 mM MOPS pH 7. VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.374	α = 90
b = 101.374	β = 90
c = 84.325	γ = 120

Symmetry
Space Group	P 62 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210	Mirrors	2008-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.979	NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.8	50	99.3	0.07	0.062	17.9	21.8		11899			105.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.9	99.6		0.333	0.361	16	21	1183

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2PIF.pdb	2.8	38.94	2	11015	1096	92.1	0.229	0.229	0.2444	0.268	0.286	RANDOM	54.4

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-12.84	2.45		-10.97		23.81

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.9
c_scangle_it	2.73
c_mcangle_it	2.49
c_scbond_it	1.73
c_angle_deg	1.4
c_mcbond_it	1.4
c_improper_angle_d	1.17
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1758
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing